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lint/dependencies/python/snakemake.txt

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Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
appdirs==1.4.4
Update Python dependencies
2023-04-16 13:02:58 -04:00
attrs==23.1.0
Update Python dependencies
2022-12-20 10:35:15 -05:00
certifi==2022.12.7
Bump charset-normalizer from 3.1.0 to 3.2.0 in /dependencies/python (#4583) Bumps [charset-normalizer](https://github.com/Ousret/charset_normalizer) from 3.1.0 to 3.2.0. - [Release notes](https://github.com/Ousret/charset_normalizer/releases) - [Changelog](https://github.com/Ousret/charset_normalizer/blob/master/CHANGELOG.md) - [Commits](https://github.com/Ousret/charset_normalizer/compare/3.1.0...3.2.0) --- updated-dependencies: - dependency-name: charset-normalizer dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-22 11:37:03 -04:00
charset-normalizer==3.2.0
Bump configargparse from 1.5.3 to 1.7 in /dependencies/python (#4659) Bumps [configargparse](https://github.com/bw2/ConfigArgParse) from 1.5.3 to 1.7. - [Release notes](https://github.com/bw2/ConfigArgParse/releases) - [Commits](https://github.com/bw2/ConfigArgParse/compare/v1.5.3...1.7) --- updated-dependencies: - dependency-name: configargparse dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-18 15:04:00 -04:00
ConfigArgParse==1.7
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
connection-pool==0.0.3
datrie==0.8.2
Bump docutils from 0.19 to 0.20.1 in /dependencies/python (#4785) Bumps [docutils](https://docutils.sourceforge.io/) from 0.19 to 0.20.1. --- updated-dependencies: - dependency-name: docutils dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-10-24 19:50:46 -04:00
docutils==0.20.1
Bump dpath from 2.1.5 to 2.1.6 in /dependencies/python (#4336) Bumps [dpath](https://github.com/dpath-maintainers/dpath-python) from 2.1.5 to 2.1.6. - [Release notes](https://github.com/dpath-maintainers/dpath-python/releases) - [Commits](https://github.com/dpath-maintainers/dpath-python/compare/v2.1.5...v2.1.6) --- updated-dependencies: - dependency-name: dpath dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Zack Koppert <zkoppert@github.com>
2023-08-10 18:20:01 -04:00
dpath==2.1.6
Bump fastjsonschema from 2.16.3 to 2.18.0 in /dependencies/python (#4509) Bumps [fastjsonschema](https://github.com/horejsek/python-fastjsonschema) from 2.16.3 to 2.18.0. - [Changelog](https://github.com/horejsek/python-fastjsonschema/blob/master/CHANGELOG.txt) - [Commits](https://github.com/horejsek/python-fastjsonschema/compare/v2.16.3...v2.18.0) --- updated-dependencies: - dependency-name: fastjsonschema dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-17 11:03:13 -04:00
fastjsonschema==2.18.0
Update Python dependencies
2022-12-20 10:35:15 -05:00
gitdb==4.0.10
Update Python dependencies
2023-04-10 14:08:31 -04:00
GitPython==3.1.31
Update Python dependencies
2023-01-22 18:34:06 -05:00
humanfriendly==10.0
Update Python dependencies (#3348) Co-authored-by: Super-Linter Automation <noreply@github.com> Co-authored-by: Marco Ferrari <ferrari.marco@gmail.com>
2022-09-26 14:48:52 -04:00
idna==3.4
Update Python dependencies (#2852) Co-authored-by: Super-Linter Automation <noreply@github.com>
2022-05-02 10:22:46 -04:00
Jinja2==3.1.2
Bump jsonschema from 4.17.3 to 4.19.0 in /dependencies/python (#4530) Bumps [jsonschema](https://github.com/python-jsonschema/jsonschema) from 4.17.3 to 4.19.0. - [Release notes](https://github.com/python-jsonschema/jsonschema/releases) - [Changelog](https://github.com/python-jsonschema/jsonschema/blob/main/CHANGELOG.rst) - [Commits](https://github.com/python-jsonschema/jsonschema/compare/v4.17.3...v4.19.0) --- updated-dependencies: - dependency-name: jsonschema dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-16 14:07:51 -04:00
jsonschema==4.19.0
Bump jupyter-core from 5.3.0 to 5.3.1 in /dependencies/python (#4658) Bumps [jupyter-core](https://github.com/jupyter/jupyter_core) from 5.3.0 to 5.3.1. - [Release notes](https://github.com/jupyter/jupyter_core/releases) - [Changelog](https://github.com/jupyter/jupyter_core/blob/main/CHANGELOG.md) - [Commits](https://github.com/jupyter/jupyter_core/compare/v5.3.0...v5.3.1) --- updated-dependencies: - dependency-name: jupyter-core dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-21 02:56:59 -04:00
jupyter_core==5.3.1
Update Python dependencies
2023-01-22 18:34:06 -05:00
MarkupSafe==2.1.2
Update Python dependencies
2023-04-10 14:08:31 -04:00
nbformat==5.8.0
Update Python dependencies
2022-04-04 09:09:03 -04:00
plac==1.3.5
Bump platformdirs from 3.2.0 to 3.5.1 in /dependencies/python (#4200) Bumps [platformdirs](https://github.com/platformdirs/platformdirs) from 3.2.0 to 3.5.1. - [Release notes](https://github.com/platformdirs/platformdirs/releases) - [Changelog](https://github.com/platformdirs/platformdirs/blob/main/CHANGES.rst) - [Commits](https://github.com/platformdirs/platformdirs/compare/3.2.0...3.5.1) --- updated-dependencies: - dependency-name: platformdirs dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-05-23 15:39:48 -04:00
platformdirs==3.5.1
Bump psutil from 5.9.4 to 5.9.5 in /dependencies/python (#4128) * Bump psutil from 5.9.4 to 5.9.5 in /dependencies/python Bumps [psutil](https://github.com/giampaolo/psutil) from 5.9.4 to 5.9.5. - [Release notes](https://github.com/giampaolo/psutil/releases) - [Changelog](https://github.com/giampaolo/psutil/blob/master/HISTORY.rst) - [Commits](https://github.com/giampaolo/psutil/compare/release-5.9.4...release-5.9.5) --- updated-dependencies: - dependency-name: psutil dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Update dependencies/python/snakemake.txt --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Philip Mallegol-Hansen <philip@mallegolhansen.com> Co-authored-by: Zack Koppert <zkoppert@github.com>
2023-05-25 18:33:01 -04:00
psutil==5.9.5
Update Python dependencies
2022-12-20 10:35:15 -05:00
PuLP==2.7.0
Update Python dependencies
2023-01-02 12:14:49 -05:00
pyrsistent==0.19.3
Bumps PyYAML to 6.0.1 (#4497) There's some conflict where PyYAML 6.0.0 and Cython 3.0 do not play well together, this version fixes that.
2023-07-21 18:04:44 -04:00
PyYAML==6.0.1
Bump requests from 2.28.2 to 2.31.0 in /dependencies/python (#4343)
2023-07-23 11:48:14 -04:00
requests==2.31.0
Update Python dependencies
2022-12-20 10:35:15 -05:00
reretry==0.11.8
smart-open==6.3.0
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
smmap==5.0.0
Bump snakemake from 7.28.3 to 7.30.1 in /dependencies/python (#4411) Bumps [snakemake](https://github.com/snakemake/snakemake) from 7.28.3 to 7.30.1. - [Release notes](https://github.com/snakemake/snakemake/releases) - [Changelog](https://github.com/snakemake/snakemake/blob/main/CHANGELOG.md) - [Commits](https://github.com/snakemake/snakemake/compare/v7.28.3...v7.30.1) --- updated-dependencies: - dependency-name: snakemake dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-06-29 20:30:42 -04:00
snakemake==7.30.1
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
stopit==1.1.2
Update Python dependencies (#3425) Co-authored-by: Super-Linter Automation <noreply@github.com>
2022-10-10 13:35:54 -04:00
tabulate==0.9.0
Update Python dependencies
2022-12-20 10:35:15 -05:00
throttler==1.2.2
Update Python dependencies
2023-04-10 14:08:31 -04:00
toposort==1.10
traitlets==5.9.0
urllib3==1.26.15
wrapt==1.15.0
Update Python dependencies (#3000) Co-authored-by: Super-Linter Automation <noreply@github.com>
2022-06-06 09:12:54 -04:00
yte==1.5.1
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